3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
4 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 <title>Jalview Command Line Arguments
22 <p><strong>The Jalview Executable's Command Line
23 Arguments</strong></p>
24 See <a href="commandline.html">running Jalview from the command
25 line</a> for more information.<br>
26 <table width="100%" border="1" cellspacing="0" cellpadding="0">
28 <td width="27%"><div align="center">-nodisplay</div></td>
29 <td width="73%"><div align="left">Run Jalview without User Interface. (automatically disables questionnaire, version and usage stats checks)</div></td>
33 <td><div align="center">-props FILE</div></td>
34 <td><div align="left">Use the given Jalview properties file instead
35 of users default.</div></td>
38 <td><div align="center">-features FILE</div></td>
39 <td><div align="left">
40 <p>Use the given file to add sequence features to an alignment.
41 See <a href="featuresFormat.html" target="NEW">Features
42 File</a> (Known as Groups file prior to 2.08) description. </p>
48 <div align="center">-annotations FILE</div>
50 <td>Add precalculated annotations to the alignment. See <a
51 href="annotationsFormat.html" target="NEW">Annotation File</a>
56 <div align="center">-tree FILE</div>
58 <div align="left">Load the given newick format tree file onto
64 <div align="center">-questionnaire URL</div>
66 <div align="left">Queries the given URL for information about
67 any Jalview user questionnaires</div>
72 <div align="center">-noquestionnaire</div>
74 <div align="left">Turn off questionnaire check</div>
78 <div align="center">-nousagestats</div>
80 <div align="left">Turn off google analytics usage tracking</div>
84 <div align="center">-[no]sortbytree</div>
86 <div align="left">Enable or disable automatic sorting of associated view when a new tree is displayed</div>
91 <div align="center">-dasserver nickname=URL</div>
93 <div align="left">Add and enable a <a href="dassettings.html">DAS server</a> with given
94 nickname (alphanumeric or underscores only) for retrieval of features
95 for all alignments<br>
96 Sources that also support the sequence command may be specified by prepending the URL with 'sequence:'<br>
97 <em>e.g.</em> sequence:http://localdas.somewhere.org/das/source</div>
102 <div align="center">-fetchfrom nickname</div>
104 <div align="left">Query a <a href="dassettings.html">DAS source</a> called nickname for features for the alignments
105 and display them</div>
110 <div align="center">-groovy FILE</div>
112 <div align="left">Execute groovy script in FILE (where FILE may be 'STDIN' to read from the standard input) after all other
113 arguments have been processed</div>
118 <div align="center">-vdoc VAMSAS DOCUMENT FILE or URL</div>
120 <div align="left">Import the given vamsas document into a new session.<br><em>New in 2.5</em></div>
125 <div align="center">-vsess VAMSAS SESSION URL</div>
127 <div align="left">Join the given vamsas session<br>If a document was also specified, this will be imported first and then committed as new data from Jalview to the specified session (Experimental - not yet enabled!).<em>New in 2.5</em></div></div>
132 <div align="center">-groovy FILE</div>
134 <div align="left">Execute groovy script in FILE (where FILE may be 'STDIN' to read from the standard input) after all other
135 arguments have been processed</div>
140 <div align="center">-fasta FILE</div>
144 <div align="left">Create alignment file FILE in Fasta format.</div>
148 <td><div align="center">-clustal FILE</div></td>
149 <td><div align="left">Create alignment file FILE in Clustal format.</div></td>
152 <td><div align="center">-msf FILE</div></td>
154 <td><div align="left">Create alignment file FILE in MSF format.</div></td>
157 <td><div align="center">-pileup FILE</div></td>
158 <td><div align="left">Create alignment file FILE in Pileup format.</div></td>
161 <td><div align="center">-pir FILE</div></td>
163 <td><div align="left">Create alignment file FILE in PIR format.</div></td>
166 <td><div align="center">-pfam FILE</div></td>
167 <td><div align="left">Create alignment file FILE in PFAM format.</div></td>
170 <td><div align="center">-blc FILE</div></td>
171 <td><div align="left">Create alignment file FILE in BLC format.</div></td>
174 <td><div align="center">-jalview FILE</div></td>
176 <td><div align="left">Create alignment file FILE in Jalview format.</div></td>
179 <td><div align="center">-png FILE</div></td>
180 <td><div align="left">Create PNG image FILE from alignment.</div></td>
183 <td><div align="center">-imgMap FILE</div></td>
185 <td><div align="left">Create HTML file FILE with image map of PNG
189 <td><div align="center">-eps FILE</div></td>
190 <td><div align="left">Create EPS file FILE from alignment.</div></td>